From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Sun Sep 09 2007 - 21:29:51 CDT
Hi Boyang,
histidine protonation is a bit more painful that just charged/uncharged,
since the question really should be whether you have delta or epsilon
protons (or both). If you want to do a good job of assigning histidine
protonation states, there are at least three possibilities:
-Use a protein protonation state prediction tool, like propka or the
combination of MEAD and mcrp. Looking through the constant-pH molecular
dynamics literature should give you a good feel for the methods that are
out there
-Manually assign the state at each histidine based on the local hydrogen
bonding environment
-Apply a heuristic based on the local potential near the delta and
epsilon nitrogens of each histidine (basically a simpler version of the
first option)
The first of those choices is certainly the most rigorous, but you can
probably do well with the other two as well, particularly for smaller
proteins
Best,
Peter
Wang, Boyang wrote:
> Dear all,
>
> green fluorescent protein, (for example, PDB ID 1W7S) has about 10
> histidines. I wonder how I could get the charged states (positively
> charged or neutral) of each histidine.
>
> One way to do it is to try different charged states and study the
> stability of the protein, which actually takes a long time.
>
> Thanks a lot for your considerations!
>
> Boyang.
>
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